H3ABioNet Postgraduate Bioinformatics Workshop 21st April-26th May 2014 Covenant University Bioinformatics Research (CUBRe), Ota Nigeria

: Training; 05 May 2014; Hits: 11559

Course Overview:

The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects.

H3ABioNet aims to create a sustainable African Bioinformatics Network to support and promote the development of bioinformatics capacity within Africa, by training the next generation of students in bioinformatics. To achieve this vision, H3ABioNet will be hosting a five week training workshop in bioinformatics aimed at students registered for a postgraduate academic degree in bioinformatics or a related discipline from the H3ABioNet Nodes and H3Africa projects from the 21^st of April to the 26^th of May 2014 at the Covenant University Bioinformatics Research (CUBRe) unit in Ota, Nigeria.

Keywords: Biological data resources, Data handling, Sequence analysis, Genomics

Skill level of training: Beginner

Language: English

Credential awarded: no credential awarded

Type of training: face-to-face / in person

Intended audience:

The H3ABioNet Postgraduate workshop is aimed at developing a core set of specialised skills amongst registered postgraduate students within H3ABioNet and H3Africa projects to provide them with practical training in a variety of introductory bioinformatics topics to complement their ongoing research and education and strengthen the bioinformatics capacity within their Node/group.

Syllabus and tools:

The H3ABioNet Postgraduate workshop will run over 5 weeks (6 days a week) and will cover both theoretical and practical aspects of a range of core bioinformatics modules which include:

Introduction to Linux
Python programming
Introduction to bioinformatics resources
Biostatistics and R
Database creation and data mining
Bioinformatics workflows and pipelines
Introduction to NGS tools and variant calling

H3ABioNet Postgraduate workshop prerequisites:

Successful applicants would be required to complete some prerequisites which may include on-line courses prior to the commencement of the H3ABioNet 2014 Postgraduate workshop. Participants would be notified of these requirements upon admission.

H3ABioNet Postgraduate workshop objectives:

The H3ABioNet 2014 Postgraduate workshop is aimed at providing post graduate students registered for an academic degree and are working on research projects with a significant component of bioinformatics with the necessary grounding in core bioinformatics topics. The H3ABioNet 2014 Postgraduate workshop aims to equip these individuals with the necessary skills to continue their ongoing bioinformatics education, further learn on topics that are of interest to them and apply the skills learnt to their academic research projects.

H3ABioNet Postgraduate workshop outline

The H3ABioNet 2014 Postgraduate workshop comprises a number of modules that will span a 5 week period and include both theoretical lectures and practical sessions for registered students to learn and develop their theoretical and practical skills and provide a foundation for participants to develop their bioinformatics knowledge. A tentative timetable for the H3ABioNet 2014 Postgraduate workshop is provided below:

Name	Topic taught	Period Topic is Taught	Dates for Topic being taught
Dr Oyelade and Mrs Itunu Isewon	Introduction to linux and Python programing	Week 1	21^st April to 25^th April
Shaun Aron	Introduction to bioinformatics resources, Sequence alignment, and proteomics resources	Week 2	28^th April to 2^nd May
Dr. Jean-Baka Domelevo Entfellner	Introduction to Biostatistics	Week 3	5^th May to 9^th May
Dr. Takafumi Yamaguchi and Dr. Lawrence Heisler	NGS	Week 4	12^th May to 16^th May
Dr. Segun Fatumo	GWAS	Week 4	16^th May, 19^th May
Dr. Kais Ghedira and Dr. Amel Ghoulia	Databases, mining and analysis workflows / pipelines	Week 5	19^th May to 23^rd May
Dr Oyelade and Miss Itunu Ewejobi	Python programming for 3 hours every day	Throughout the workshop	28^th April to 24^th May

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19105511. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

past , bioinformatics introduction

H3ABioNet NABDA Node Training Course on Visual Analytics of Human Genome Variation Datasets

: Training; 08 December 2013; Hits: 10782

Course Overview: The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent.

Catalogues on human genome variants produced by large-scale human genome variation projects provide a wealth of genome variation datasets to conduct research on the genomics and environmental determinants of common diseases with the goal of improving the health of African populations. A recognized need is to promote computational skills among African researchers to facilitate genomics-based research on human disease and health across the continent. Visual analytics, the science of analytical reasoning supported by interactive visual interfaces, provides computational tools and techniques to foster collaboration in making sense of data of any size. Participants will be introduced to the focus areas of visual analytics and learn visual analytics skills by working with datasets from catalogues on human genome variation such as 1000 genomes, National Human Genome Research Institute (NHGRI) GWAS Catalog and the Database of Genomic Variations. The expectation is that participants will initiate collaboration among the H3Africa consortium projects. The course is open to staff and students in the H3Africa Consortium projects.

The successful applicant’s home institution/project shall be responsible for transportation (to and from Abuja), and accommodation (Bed and Breakfast) at Abuja, and dinners during their stay. The host institution (NABDA/FMST) shall provide, in addition to free tuition, Tea Breaks and lunches during the course.

Course Trainers
Dr. Raphael Isokpehi, Visual Analytics in Biology Curriculum Network, USA
Dr. Oyekanmi Nash, NABDA, Nigeria
Dr. Segun Fatumo, NABDA/SANGER
Atinuke Hassan, NABDA, Nigeria

Course Programme
Day 1: Monday, 29 July, 2013
Bioinformatics Research Categories
Definition, Focus Areas, Scope and Process of Visual Analytics
Hardware and Software for Visual Analytics
Hands-on Exercises

Day 2: Tuesday, 30 July, 2013
Introduction to Datasets of Catalogues on Human Gene Names
Hands-on Exercises

Day 3: Wednesday, 31 July, 2013
Introduction to Datasets of Catalogues on Human Genome Variation
Hands-on Exercises

Day 4: Thursday, 1 August, 2013
Collaborative Visual Analytics
Day 5: Friday, 2 August, 2013
Collaborative Visual Analytics
Course Evaluation

How to apply

To apply to attend the course please complete the application form found here:
http://surveys.h3abionet.org/visualanalytics
The application form will open on the 25th June and the deadline for applications is the 15th July 2013.
Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached

Training Materials Availability:

Training materials for this course are not currently available.

past , education

H3ABioNet Train-the-Trainer Bioinformatics Course 8th – 26th July 2013 International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya

: Training; 08 December 2013; Hits: 12718

Course Overview: The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. The H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent. To achieve this vision the H3ABioNet will be hosting the first specialized bioinformatics training course for bioinformaticians and researchers within the network.

The course is aimed at developing a core set of specialised skills amongst members in the network who are in a position to train others at their institutions. The course will train members who are required to efficiently manage and analyse the vast amount of genomic data generated by the various H3Africa projects.

The course will be run over 3 weeks (6 days a week) and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genomic and population-based data. An emphasis will be placed on allowing participants to develop hands-on experience with analysing real data using open source software, tools and resources.

The course is open to all members within the H3A Bioinformatics Network, who have long term positions at one of the partner institutions and the capacity to train others in their institution when they return from the course.

Course objectives

The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to manage and analyse genomic data. As well as specialized topics in population genetics, GWAS and next-generation sequence analysis, the course will include programming to ensure participants gain basic skills in data manipulation and management, and biostatistics to prepare them for statistical analysis of data.

Course outline

Programming using python – basic introduction through to advanced topics for managing and manipulating biological data. Will be run for 2 hours every morning for the duration of the course.

Introduction to Linux – basic history and introduction through to complex commands for manipulating data and Bash scripting

Data management – building simple MySQL queries and introduction to BioMart

Biostatistics – basic probability theory, introduction to R, statistical hypothesis testing, principal component analysis, building regression models and visualisation

Population genetics – content to be confirmed

Genome-wide association studies – content to be confirmed

Next-generation sequencing – introduction and QC, assembly and reference genome alignment, variant calling, RNA-seq data analysis, ChIP-seq data analysis, genome visualisation

Course prerequisites

Each course component will have prerequisites that participants will be required to complete or fulfill before the course starts. Participants will be notified of these requirements before the course commences.

How to apply

To apply to attend the course please complete the application form found here:

http://surveys.h3abionet.org/icipe

The deadline for applications is the 17th May 2013.

Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached.

For those who are unable to attend the course in person, there will be the possible option of joining the course via live streaming to Tunis (Institut Pasteur) and IBADAN (NABDA-Southwest Center, University of Ibadan).

Training Materials Availability:

Training materials for this course are not currently available.

past , education

H3ABioNet Introduction to Bioinformatics using the eBioKit platform 29th of July to 2nd of August 2013 International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya

: Training; 08 December 2013; Hits: 10054

eBioKit is a system for teaching bioinformatics, which is running multiple open source web services on an Apple Mac-mini where all databases are stored locally. This reduces the need for a fast internet connection while giving the users an opportunity to incorporate their data sets in widely used web services.
This course is aimed at familiarizing trainees with the multiple uses of ebiokit. The course will train members who are required to perform bioinformatics analysis of genetic and genomic data generated in the various H3Africa projects but most likely also in other projects in there respective institutions.
The course will be 5 days long and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genetic and genomic data. An emphasis will be placed on allowing participants to develop hands-on experience with analyzing real data using ebiokit.
The course is open to all members of the H3A Bioinformatics Network as well as H3A Researchers who are seeking advanced bioinformatics training.

Course objectives

The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to analyze genetic, genomic and metagenomic data. The course will include some basic linux programming and then offer a comprehensive overview of commonly used bioinformatics tools and databases available on the eBiokit system, such as for example Ensembl and Galaxy, a Web-based platform for data-intensive biomedical research.

Trainers

Prof. Erik Bongcam-Rudloff, SLU-Global Bioinformatics Centre, Sweden
Dr. Andreas Gisel, Institute for Biomedical Technologies, Italy
Dr. Anne Fischer, ICIPE, Kenya
Dr. Etienne de Villiers, KWTRP, Kenya
Rafael Hernández, Centro de Investigaciones Príncipe Felipe

Course programme

Monday

Introduction to Bioinformatics
How to use the eBioKit
UNIX command line

Tuesday

Introduction to Biological Databases
Basics of Blast search
Constructing your own searchable blast database
MRS: searching with names and keywords
Introduction to Genome Browsers: Ensembl: part 1

Wednesday

Exploring ENSEMBL functionalities: part 2
EMBOSS (the European Molecular Biology Open Software Suite):
Alignments, global, local
Searching with motifs and more
Multiple alignments
Introduction to Phylogenetics